Pope John IX (Latin: Ioannes IX) was Pope from January 898 to his death in 900.

With a view to diminish the violence of faction in Rome, John held several synods in Rome and elsewhere in 898. They not only confirmed the judgment of Pope Theodore II in granting Christian burial to Pope Formosus, but also at a council held at Ravenna decreed that the records of the synod held by Pope Stephen VI which had condemned him should be burned. Re-ordinations were forbidden, and those of the clergy who had been degraded by Stephen were restored to the ranks from which he had deposed them. The custom of plundering the palaces of bishops or popes on their death was ordered to be put down both by the spiritual and temporal authorities.

To keep their independence, which was threatened by the Germans, the Slavs of Moravia appealed to John to let them have a hierarchy of their own. Ignoring the complaints of the German hierarchy, John sanctioned the consecration of a metropolitan and three bishops for the Church of the Moravians.

Finding that it was advisable to cement the ties between the empire and the papacy, John IX gave unhesitating support to Lambert in preference to Arnulf during the Synod of Rome, and also induced the council to determine that henceforth the consecration of the Popes should take place only in the presence of the imperial legates. The sudden death of Lambert shattered the hopes which this alliance seemed to promise.

John IX died in the year 900 and was succeeded by Pope Benedict IV (900 - 903).